SCAF11 / SRrp129 (Q99590) - an SR-related protein that binds the RNA Pol II CTD, in the pan-MLL-fusion core, and alone among the SCAF family

SYSTEM: the AP-MS host is JURKAT, a human T-ALL line, while KMT2A::AFF1 disease is B-lineage infant leukaemia; a partner requiring a B-cell or infant proteome cannot appear here and a T-lineage partner can appear spuriously. The bait is a Strep-HA-tagged, SINGLE-COPY, doxycycline-induced transgene at an FRT/Flp cassette, not the endogenous fusion. Prey came from bulk nuclear lysate (buffer C420, 420 mM NaCl) after a single STREP-Tactin step, so co-purification is NOT evidence of a direct contact. INCLUSION RULE: the paper kept the top 300 interactions per bait by combined p-value rather than applying a p threshold (Methods, verbatim: "All the identified bait-prey pairs were ranked by the combined p-value. The 300 most significant interactions per bait were retained."). Measured by this beat from the cached MOESM4 xlsx on 2026-09-21: 545 of the 2,049 per-bait p-values in the table (26.6%) exceed 0.05; within the MLL-AF4 column alone it is 186 of 291 (63.9%), and that column's maximum p is 0.175. MEASURED BY THIS BEAT, 2026-09-21, from the cached MOESM4 xlsx: across all 42 pan-fusion proteins the MLL-AF4 column carries the LOWEST total spectral counts of the seven baits for 34 of 42, and is sixth or seventh for 40 of 42. That is a bait-level property (transgene expression, purification depth or the DDX5/DDX17 GLM normalisation), not a statement about any one prey, so a low MLL-AF4 count must not be read as a weaker association than the same protein's count under another bait. For SCAF11 the MLL-AF4 total (13 spectra over two replicates) is rank 7 of the seven baits, against a maximum of 34 under another bait. All seven per-bait values, p (replicate spectral counts): MLL-AF1p 0.0068 (11|3); MLL-AF4 0.0013 (6|7); MLL-AF9 0.0001 (17|17); MLL-CBP 0.0119 (3|14); MLL-EEN 0.0008 (15|16); MLL-ENL 0.0001 (17|16); MLL-GAS7 0.0116 (13|7). SPECIFIC TO THIS PROTEIN: at p = 0.00125 this is the strongest MLL-AF4 call in this tranche and one of the stronger ones in the 42, with six of seven baits at or below 0.012 and a clean 0|0 negative control. The weakness here is not the statistics - it is that almost nothing is known about what this paralogue does, so a strong row on a poorly characterised protein buys less than it appears to. SELECTIVITY: the paper's named non-selectivity controls are RFC1, SF3A3 and CCT3 - knockdown inhibited MLL-wild-type K562 and HL-60 as much as MOLM-13 - against MEN1 as the selective positive. Only 40 of the 128 ('the 40 candidate genes with the highest confidence') entered that MLL-r versus MLL-wild-type re-screen, and the paper does not list which 40. This protein is not named among the controls, but that is NOT evidence of selectivity: it is equally consistent with the protein never having reached the second screen. Recorded as unknown, and this entry must not be read as nominating a target. Values re-read from the cached xlsx on 2026-09-21 and cross-checked against analyses/skucha-mll-fusion-interactome/results.json, whose two controls (128 proteins shared by >=5 baits and 42 by all seven, both matching the paper; MEN1 present with all seven) both PASS on today's re-run.

• IntAct has never curated this dataset, so no independent curator has re-examined these calls and no interactome-coverage metric built on IntAct can see them; the raw spectra at ProteomeXchange PXD009338 have not been reanalysed here. The authors themselves removed seven proteins from the shared set by hand as 'either frequently observed contaminants or ... not detected in human hematopoietic cell lines', which concedes that the rank cutoff lets contaminants through - and ACTB survived that filter, sitting in the pan-fusion 42 with a NON-ZERO negative control (3|3). Ten of the 42 carry a non-zero negative control: PSIP1 0|5, MCM2 0|2, ACTB 3|3, CSNK2A1 2|0, RUNX1 0|2, SF3A3 0|3, TCEB3 0|1, CHD4 2|2, SMARCC1 1|0, ZNF512 0|2 - counted by this beat from the xlsx neg_ctrl column, 2026-09-21. ProteomeXchange/PRIDE 2018
• The paper states that 'more than one third of proteins in the network of conserved MLL-fusion protein interaction partners were identified as essential in recent genome-wide screens'. Abundance and essentiality both raise the odds of recovery in an AP-MS experiment, so membership in the conserved core is partly a statement about how much of a protein is present in a nucleus, not only about what it binds. Skucha A et al. 2018

1996; yeast two-hybrid plus co-immunoprecipitation from nuclear extract plus an in vitro splicing inhibition assay. The proteins identified were RAT; the paper defines the SCAF family rather than characterising SCAF11 specifically. Yeast two-hybrid is a heterologous binary assay with a well-known false-positive rate. Not haematopoietic, not a fusion system. Read from the abstract.

• Three decades on, the individual SCAF paralogues have turned out to have separable functions - SCAF4 and SCAF8 at cleavage and polyadenylation, SCAF1 as an elongation activator - so the family-level conclusion of 1996 does not transfer to SCAF11 in particular, and no modern loss-of-function study of SCAF11 exists that this beat could find. Tanner S et al. 1997

1997, Biological Chemistry; yeast two-hybrid with a phosphorylated CTD-GAL fusion bait. This is the paper that names this protein - SRrp129/CASP11 is Q99590 - and it is essentially the only characterisation of it. A binary interaction in yeast is not a cellular interaction. Not haematopoietic, not a fusion system. Read from the abstract. The 'SC35-interacting protein 1' name carried by UniProt derives from a separate reported SRSF2 contact that this beat did not verify to a primary source.

• The screen bait was a phosphorylated CTD expressed in yeast; the authors themselves note this is why they recovered processing factors rather than initiation factors, so the result is partly a property of the bait's phosphorylation state and does not establish which Pol II state SCAF11 engages in a human cell. Yuryev A et al. 1996

Murine and human MLL-rearranged leukaemia; the abstract does not name which fusions, so this is 'MLL-rearranged' and not specifically KMT2A::AFF1 or infant B-lineage. Cited here for ONE purpose: to establish that a splicing dependency in this disease is real, so that splicing-adjacent interactome rows are not dismissed out of hand. MBNL1 is NOT in the Skucha 960-protein network at any n and neither is PTBP1 (checked by this beat from the xlsx, 2026-09-21), so this paper's protein and this entry's protein are unrelated. Read from the abstract.

• That the validated splicing dependency in MLL-rearranged leukaemia is a protein ABSENT from the fusion interactome cuts against the interactome as a route to splicing biology here: the dependency was found by expression and function, not by co-purification, and the co-purified splicing proteins have no dependency data at all. Skucha A et al. 2018